Interdisciplinary analyses of Bronze Age communities from Western Hungary reveal complex population histories, Gerber et al.
Abstract
In this study we report 20 ancient shotgun genomes from present-day Western Hungary (3530 - 1620 cal BCE), mainly from previously understudied Baden, Somogyvar-Vinkovci, Kisapostag, and Encrusted Pottery archaeological cultures. Besides analysing archaeological, anthropological and genetic data, 14C and strontium isotope measurements complemented reconstructing the dynamics of the communities discovered at the site Balatonkeresztur. Our results indicate the appearance of an outstandingly high Mesolithic hunter-gatherer ancestry in the largest proportion (up to ~46%) among Kisapostag associated individuals, despite this component being thought to be highly diluted by the Early Bronze Age. We show that hunter-gatherer ancestry was likely derived from a previously unrecognised source in Eastern Europe that contributed mostly to prehistoric populations in Central Europe and the Baltic region. We revealed a patrilocal residence system and local female exogamy for this Kisapostag population that was also the genetic basis of the succeeding community of the Encrusted Pottery culture, represented by a mass grave that likely resulted from an epidemic. We also created a bioinformatic pipeline dedicated for archaeogenetic data processing. By developing and applying analytical methods for analysing genetic variants we found carriers of aneuploidy and inheritable genetic diseases. Furthermore, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin.
https://www.biorxiv.org/content/10.1101/2022.02.03.478968v1
___________
I'll later update this post.
PS
Bk-I: Somogyvár - Vinkovci culture S9 2560-2290 35-40 M K1a3a R1a-V2670 None
Comments
The mystery of the Balto-Slavic drift is solved. You talked about it a long time ago.
Can you do me a favour and correct this piece of disinformation ("Also it seems this result is based on Str results or? so I remain skeptical") on AG?
From the paper ("Bioinformatic analyses" section):
"For Y chromosome haplogroup determination the Yleaf v1 software was applied."
I discovered it when modeling the Mokrin set. After picking out the HG-rich outliers, I made an average out of them. Again, at that time, I just assumed this HG ancestry to be the “usual” Iron Gates WHG or smth. After failing to get a decent fit, I attributed this to presumed poor coverage. But some time later, I tried Baltic_Ba for the heck of it and....voila. [Insert apt meme here] I had to look at it twice. lol
This then prompted me to run other existing Carpathian BA samples and, sure enough, some of them also exhibited this and gave me substantially better fits than I’d achieved previously. When the Slavonia Jag samples came out—-same exact.
Long story short, I’ve had to rethink my prior paradigms, and, just like you guys, I also see Baltic_BA ancestry moving in a south-north direction. For existing Baltic_Ba samples—-Probably some epi-corded derived Mierzanowice-related groups residing on the northern foothills are the direct culprit, if I had to guess? As for the southern foothill(of the northern chain) populations like Encrusted Ware, I think an independent formation occurred. I.e. I don’t think Baltic_BA-like pops crossed the Carpathians from the north to create the Encrusted. They were a local merger of EEF, uncanny HG, and Hyperborean-rich incomers.
When you think about it, it’s unsurprising that an uncanny HG population existed somewhere in the Carpathians or their foothills. That kind of thing provides obvious refuge to older population strata, for one.
And MASSIVE kudos to you guys—-Arza and Ambron——for also noting this. I discovered your blog a couple of weeks ago in an attempt to find other individuals who also made this observation. Always good to level with the like-minded. We are almost there, but we will be vindicated in full one of these years when they dig up our sought-after HGs in the Beskids(?). Heck, more Vatya_outlier samples would be excellent, too.
Dinner is all on Dave lol
Scroll down a tiny bit and see fig 1:
https://www.semanticscholar.org/paper/Funeral-rites-on-the-southern-boundary-of-the-Romaniszyn-Niculică/22192f4f8a0d2d1833a0de2d9db39f8c35a1e729
I never understood why anyone would try to explain it as a purely Bronze Age phenomenon. Especially not after the study about the origin of Icelanders was published. If anyone wants to see how a 1000 years of a genetic drift on an isolated island looks like just compare Icelanders to Norwegians. That's nowhere close to the so-called Balto-Slavic drift.
Although there are two layers of this drift, but that's another story - Palaeolithic (practically everyone in Europe has it) and Mesolithic (characteristic to certain BA populations and modern day Balto-Slavs and pops mixed with Balto-Slavs).
IMHO the origin of Baltic_BA and generally the history of Indo-Slavs as EastPole calls them is pretty straightforward - early Indo-Europeans move towards the Carpathians and acquire some additional EEF ancestry. Future Indo-Iranians immediately bounce off the Carpathians (main Nitra cluster is identical to Fatyanovo). Future Balto-Slavs cross the mountains... and now we have two possibilities:
a) Balto-Slavs acquire HG ancestry and to-be-Balts move north, while to-be-Slavs stay near the Carpathians and they start to acquire low-WHG EEF ancestry,
b) Balto-Slavs split, to-be-Balts mix with almost pure HG, while to-be-Slavs mix with a population on an EEF-HG cline.
Later the Balto-Slavic cline (as seen on the North Euro PCA) develops - Proto-Slavs shift towards Baltic_BA while Proto-Balts slowly acquire "southern" admixture that differentiates them from Baltic_BA.
Previously I thought that such HG refuge was north of Ukraine. But now we have plenty samples from the Baltics - no HGs can be the source of the drift, we have plenty samples from Volosovo... not only they lack the drift, but they're EHG-like. Finally we have Fatyanovo that rolled over the whole area and again - no sign of the population we're looking for. On the other hand the Balto-Slavic drift explodes in the BA in the Carpathians and surroundings in a multitude of loosely connected cultures which indicates that the source of this ancestry had to be local.
Kudos also to Matt. Years ago he first noted that the Balto-Slavs deviate from other Europeans in the sixth dimension of the West Eurasian PCA made by Davidski.
The best moment for me was when it became clear that I've indeed discovered the Baltic_BA population. Months before Mittnik et al. published the preprint I already had calculated coordinates of this population. Later, when Davidski added them to the WE PCA, my ghost has landed inside the Baltic_BA cluster. From that point I knew what happened in the BA in this part of Europe, because the solution was only one...
Yep... there's another Vatya outlier. He's close to the Baltic_BA, and he's very similar to VLI051. I suspect that this sample comes from one of the inhumations described here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0254360
That Fig. 1 may be very important. But there was also a lot of interaction across the mountains (e.g. Fuzesabony culture had settlements in South Poland).
My origin theory is similar. I also see an initial "Indo-Slavic" nucleus forming in the south of Poland with a composition similar to that of Fatyanovo before ancestors of the latter "bounced off" as you say. However, I don't necessarily see the ancestors of Balto-Slavs *crossing* the chain to acquire the uncanny HG. Instead, I favor the idea of these HGs initially co-existing in tandem with the early "Indo-Slavs", albeit occupying a different phytogeographic niche(Carpathian foothills vs Polish lowlands). Later on, I envision a fusion taking place in southern Poland/W. Ukraine, leading to the creating of Baltic_BA-like, which then expands and blankets much of NE Europe.
As for Slavs---I think their deviation from Baltic_BA is mostly explained by much later---LBA, IA, or even LIA---flux from Pannonia or, ultimately, Balkans proper into what's today Polesia. Probably related to the major introduction of J2b2 and most especially E-V13 into the early Slavic Hg pool. In fact, could be related to the late E-V13 bloom in the Carpatho-Balkan region in general. As a side note, a poster on AG named George once wrote smth about "Thrakoid" toponyms all the way on the Dnieper, but perhaps it's more related more to MBA pre-proto-Thracian populations rather than any reflux from south of the Danube. For what it's worth, Polesians and southern Russians tend to visibly, albeit somewhat equivocally, favor Bgr_IA and/or Nort_Gheg-sans-Slav input over available, chronologically older Pannonian strata like Hrv_MBA or Mokrin. Modern Polish get away with the latter, but then again, West Slavs assimilated "Westish" populations which could be offsetting things.
Btw, we actually have what are likely to be medieval Balts in our sample sets. In the Viking period set, there are ~5 individuals who are almost entirely Baltic_BA by ancestry. I can point these out later on tomorrow when I get to my files and/or share aggregate coords. These certainly are either Balts or some sort of Finnicized Balts. Modern Balts deviate substantially from them, and the most likely reason imho is massive influxes of Slavs into Baltic cities during PL Commonwealth rule from Poland proper or Rus lands. This is historically attested.
Wow, good catch on VLI051! I missed that one. There's also an IA sample like this from SVK or CZE(I forget) from the recent La Tene paper and he's R1a as well. But, in the supplement, it doesn't really say anything about VLI051 being of Vatya provenance. I tend to think of him as just a northern sub-Carpathian fellow somewhere due east of Bohemia.
I also have a question----is the Volosovo and/or actual Nitra data public? I think I vaguely recall a paper on the former(tho Dave didn't make coords), but would be interested on seeing the Fatyanovo-like Nitra!
And, given the overall discussion, what do you think of the general idea in this piece? I'm not sure about the *exact* wording of their conclusion per se, but given what we now (virtually) know about this so-called Balto-Slavic drift, I think it's not unreasonable that pre-proto-Moeso(?)-Albanoid and Balto-Slav ancestors experienced some contact in the circum-Carpathian zone. This isn't something that die-hard Illyricists wanna entertain, ofc.
https://www.lituanus.org/1993_2/93_2_05.htm
To forestall this, it would be good to point out to folks that Encrusted Ware seems to have been a dead end, a flash in the pan south of the Danube. HRV_MBA and IA from Pannonia virtually lack this signal(the I2a-Din individual who harbors it seems to be mis-dated b/c of age discrepancy of mtDNA on Y-full and he wasn't properly radio-carbon dated either). Even if we create artificial coordinates consisting of diluted Baltic_BA and/or diluted Encrusted and "force" the former to use them, fits suffer visibly. Plus, Bgr_IA lacks this, too, as do Viminacium individuals most likely but we'll soon see for sure when it's published.
Will do! Always great to see academics like yourself willing to work with us hobbyists. While you guys clearly have a definitive edge over us in your technical knowledge, sometimes we tend to have a more complete, multidisciplinary picture of things. Really, I wish you the best of luck in your work and hope you publish follow-up data and studies on this!
Global25 is a powerful tool if appropriately used and covers a lot of wavelengths. It's not useful for capturing extremely fine-scale drift(we have IBD-based tools for that, right?) and, on the other extreme, it's not always useful for inferring and/or deducing % of missing, deeply-diverged streams of ancestry(e.g. non-Eurasian ancestry in Iberomaurisians). But other than that, you can learn a LOT with it. Unfortunately, you see a lot of amateurs nowadays without a proper grasp of it nor archaeology/history and bastardize it for the most random calculator schemes(yes, $$$ schemes too) imaginable.
I do have a request for you: if sharing seq data from your paper is not an option at this time due to understandable reasons, can you by any chance project some previously-published Carpatho-Pannonian BA samples onto your PCA? In particular, the Encrusted Ware (Jag) set from this paper(but not limited to it):
https://www.nature.com/articles/s41598-021-94932-9
Also, has your team or colleagues definitively planned to examine samples from other sites in the region at this point? Should we be looking forward to more? Keep us posted.
Hello! This was less expected than the Spanish Inquisition!
I'll have a lot of questions and suggestions.
There's really a lot of things to talk about. One is that you can easily widen the scope of the publication (or write a follow-up) to "The origin of European Hunter-Gatherers" or similar.
Another thing is the difference between our "amateurish" tools and qpAdm/f-stats. This whole thing was flying under radar for so long because what is obvious in "our world", is barely visible in the "pro" tools.
Later today I'll go trough the preprint one more time and post some questions.
BTW which email is best to use to contact you?
I would like to take this opportunity to ask you, when can we expect the publication of samples from Nitra? We saw in the slides that many of them have the same specific type of HG and that many of them are Z280.
“Future Indo-Iranians immediately bounce off the Carpathians (main Nitra cluster is identical to Fatyanovo). Future Balto-Slavs cross the mountains...”
It looks like Indo-Slavs were one population derived from R1a CWC groups in Southern Poland.
What puzzles me is why Balto-Slavic drift in Europe affected R1a CWC groups and didn’t affect R1b CWC/BB groups?. The general idea of that puzzle is presented here :
https://postimg.cc/w3vXJ6GN
One possible answer is that there were no linguistic, cultural, or religious barriers between R1a CWC groups i.e. all those red dots were speaking languages which were at least partially mutually intelligible.
Another interesting problem is cremation. It looks like Somogyvár-Vinkovci culture used cremation. Later cremation became popular also north of the Carpathian mountains and finally reached Sintashta/Andronovo.
Cultural links between Southern Poland, Hungary and Sintashta are known:
https://postimg.cc/DWPt1kWZ
I should point out that Jag_MBA's HG shift is strongly, but not ENTIRELY attributable to the uncanny drift we're all hunting for.
Long story short, G25 is pretty good at picking up relatively diverged streams of ancestry to the extent that if your model is lacking the basics, it will let you know.
Using a setup sufficiently accounting for pretty much all possible relevant ancestral streams(ideally, models should only include the sufficient without duplicate and/or highly similar streams), we can see what happens when we ablate the typical WHG input:
Complete:
Target: HRV_Jag_MBA
Distance: 1.2166% / 0.01216646 (this is an excellent Euclidean distance)
44.8 HUN_Baden_LCA
31.6 Baltic_LVA_BA
12.8 CWC_Pol_PCW
10.8 ROU_Iron_Gates_HG
Ablated:
Target: HRV_Jag_MBA
Distance: 2.4842% / 0.02484217 (the absolute value is relatively bad and, most importantly, shows a large CHANGE in fit from the above)
47.4 Baltic_LVA_BA
44.2 HUN_Baden_LCA
8.4 CWC_Pol_PCW
When we are dealing with averages of relatively tight convex hulls and good overall genomic coverage per individual, such a change in fit always signifies something.
The result almost hints at there being a HG cline across the Carpathian chain, whereby some groups ended up with somewhat variable proportions of standard WHG vs uncanny HG. Although I did not read the preprint to the T(yet!), I remember it mentioning something along the lines of multiple HG sources being taken up with qpAdm attempts. So, I wonder if the above models would also hold true for Bk-II, and, if so, may explain the multiplicity in part.
To those wondering whether the Iron_Gates_Hg is merely just covering for uncanny HG ancestry and if this is a glorified overfit: Hard Nay. First of all, if that was the case, we wouldn't be left with any spare CWC in the model, as it would all be "sponged up" by Baltic_BA, which is roughly 30% HG-70% CWC. So, if we do the math above 10% would translate into ~30% Baltic_BA. If a population consists of at least 30% Baltic BA-like ancestry, attempted substitutions always result glaring and statistically significant fit worsening. & G25 ultimately operates on the best fit principle.
Plus, this feature is also true for other Carpathian samples---incl some from Mokrin.
Other pops with other haplogroups were affected too (almost all the BA pops from the inner Carpathians). But it seems that the "Celts" and others rolled over them in the IA and this ancestry survived only in the R1a-rich Balto-Slavic related populations in the outer Carpathians and further north.
Unless there was a continuation of it in Slovakia or Hungary, but only Daniel can answer this question.
Technically you're not the only one. There's another group... but they seem to be not fully aware what they've found.
Demogenomic modeling of the timing and the processes of early European farmers differentiation, Marchi et al.
https://www.biorxiv.org/content/10.1101/2020.11.23.394502v2
IMHO "West Meta" is the population we're looking for. They believe that Iron Gates branched off it, but I see this differently. Judging by what G25 shows Iron Gates is rather a 60:40 mix between the Villabruna cluster and West Meta. This is in line with their simulation (Fig 3., panel B):
https://www.biorxiv.org/content/biorxiv/early/2021/11/15/2020.11.23.394502/F3.large.jpg
In fact not only the Iron Gates seems to shifted in this direction, but the whole so-called ANE-WHG cline is bent (or rather consists of a series of clines):
https://i.postimg.cc/qMxNSrvy/ANE-WHG.png
What is even more important to this topic - such hypothetical population is in the almost exact place required to "produce" Baltic_BA cluster.
You can play with that 3D plot here: https://vahaduo.github.io/3d/g25/westeurasia/
My theory is that this unusual HG ancestry comes from another refugium (as in Marchi et al.) and that in the East it merged with ANE forming EHG, and in the Balkans it merged with expanding WHG-proper forming Iron Gates / Narva like population. Then mostly EHG pops with mostly IG-like pops started to form the HG-cline as seen on the West Eurasian PCA.
And such ancestry had to survive somewhere near the Carpathians, because it explodes there in the Bronze Age. Although there's one catch. If you switch PC3 to PC6 in the 3D plot, Baltic_BA lands in a much more extreme position. My explanation is that the "larger" PC3 shows the drift up to the Mesolithic, and the more recent drift that happened when our population X has been already isolated is dumped on the sixth dimension.
„Other pops with other haplogroups were affected too (almost all the BA pops from the inner Carpathians). But it seems that the "Celts" and others rolled over them in the IA and this ancestry survived only in the R1a-rich Balto-Slavic related populations in the outer Carpathians and further north.”
Yes, but only pops with R1a and drift managed to get out of Hungary and affect all other R1a rich Indo-Slavic pops, except those which earlier migrated east.
R1b pops with drift didn’t get out of Hungary and didn’t affect other R1b rich pops. Like BBs with drift in Hungary didn’t affect other BBs in the west.
This may suggest that R1a pops acquired the drift but didn’t change language and culture and could interact with other R1a pops without the drift passing that drift to them.
Ah. Now I understand.
But I'm not sure if such spread of this kind of ancestry would be possible without at least partial population replacements (in the Baltics Baltic_BA almost certainly replaced everyone else who lived there before).
Unless the population density in Poland, Belarus etc. was much lower than in Hungary. Do we have any estimates for this period?
We have (at least) one Volosovo sample and a rumour that the rest looks the same. In case of Nitra and another Vatya outlier we have a quasi-PCA (f3 vs. f3) from EAA presentation made by Anna Szecsenyi-Nagy. It matches West Eurasian PCA very well and has plenty of other samples so it's easy to figure out everything.
“But I'm not sure if such spread of this kind of ancestry would be possible without at least partial population replacements (in the Baltics Baltic_BA almost certainly replaced everyone else who lived there before).
Unless the population density in Poland, Belarus etc. was much lower than in Hungary. Do we have any estimates for this period?”
CWC in Northern Poland, Belarus, Baltics were mostly herders switching to hunter-gatherer lifestyle often, so population density was low.
In Southern Poland and Western Ukraine it was different but there CWC R1a had to compete for good arable land with mixed Globular Amphora, Funnelbeaker, Baden, Tripolye, BB, CWC R1b groups etc.
I see drift expansion as mixed R1a CWC farmers with drift coming from the south and replacing R1a CWC herders and hunter-gatherers without drift (i.e. they spoke similar languages and could mix). And by this they became strong enough to compete with mixed Globular Amphora, Funnelbeaker, Baden, BB and CWC R1b groups. As a result Balto-Slavic became the dominant population in Eastern Europe.
Here are other examples of Carpathian basin individuals who show a requirement for a *standard* WHG-rich source(can use Iron Gates).
I highlighted the ones who co-require uncanny HG input, behaving much like Jag.
HUN_Mako_EBA_o:I1502
SRB_Mokrin_EBA_Maros:MOK30
SRB_Mokrin_EBA_Maros:MOK22
SRB_Mokrin_EBA_Maros:MOK19A
SRB_Mokrin_EBA_Maros:I23207
Scythian_HUN:I20743
Scythian_HUN:DA194
(Now, despite equivocal need of Baltic_BA for the unhighlighted two, I still think they carry it, albeit to a lesser degree—-not unusual in clinal contexts.)
Interestingly, judging from Scythian period samples, this kind of differentiation persisted for over a millennium.
This variation is simply the result of Baltic_BA not being the actual source (too much steppe), and these samples being mixed with local steppe and eef to various degrees.
This ancestry in Pannonia is from a single source, the closest proxy among the available samples is the Mezocsat outlier (and the Vatya outlier, but he's low quality). You should be able to model all other Panonians with the Mezocsat outlier and various local influences.
Mostly beg to differ...
I mean, you do raise a good point and one I've pondered: we are lucky in the sense that virtually none of our samples really has an excess of HG of discussion in relation to CWC-related ancestry---except for Vatya_o. Were this not the case, then our fits would be quite off, indeed.
But again, this isn't the case in our case. We're looking at a non-artifactual combination of uncanny HG AND "standard" WHG ancestry in a good number of these individuals. Without getting into the specifics of G25's fidelity in discriminating supra-threshold levels of divergent streams, look at my model of Jag average above. As you can see, there is still CWC left over. If Iron Gates was really compensating for what you're contending, we wouldn't see that. And EVEN IF such a compensatory scenario was at hand, the fit would be NOWEHRE NEAR being that crisp at all. Missing 10%HG is like substituting the 30% Baltic_BA in a population like Macedonians for Hyperborean proxies lacking this drift.
We have no real basis on which to assume any single source, especially since while we have smth like Vatya_O, we also have smth like Koros_HG. While an outlier in its local EEF bio-cultural context, it's enriched for standard WHG and is therefore further suggestive of the cline in HG ancestry I make the case for.
That leftover CWC is also just a part of the compensation for JAG_MBA.
You have to take into account different components which G25 can tell apart, and their amounts within Baltic_EST_BA and JAG_MBA. In this case it's just Steppe, WHG, EEF and "Balto-Slavic" drift , for both.
Let's look just at the steppe. Baltic_EST_BA is ~60% steppe, and JAG_MBA is ~30%.
There is ~30% Baltic_EST_BA in your model, so it brings less 20% steppe into the model.
So, additional steppe has to be added to compensate.
Koros_HG is from a whole different period. he is from the early neolithic and nothing like him appears afterwards, in the middle neolithic, late neolithic, etc. There are only regular neolithic farmers for a long time. Then these WHG-rich Pannonians appear as newcomers in the EBA.
I think I'd misunderstood what you were saying and possibly vice versa. I'd initially thought you meant that *WHG* seen in my model is either compensating for cryptic HG ancestry(due to Baltic_BA's ratio of CWC:HG) or an artifact overfit for it. But it looks like we're on the same page that WHG and HG inherent to Baltic_BA are not interchangeable in terms of G25's discrimination(at least, not above a fairly low threshold).
But, no, I'm not saying that a *Baltic_BA*-like was the ACTUAL source in the spread of such drift in Pannonia. I simply use it as a vessel for the yet-to-be characterized HG ancestry. Thanks to sufficient "steppe" ancestry in all samples, things work out.
I do agree the ACTUAL immediate source of Jag_MBA's HG ancestry was probably smth akin to Vatya_outlier, not Baltic_BA-like. But my point is that similar HG-rich populations across the Pannonian basin could have easily varied in the exact composition of their HG. Some were more enriched for WHG proper, others more for "balto-slavic" HG. (As a result, the resultant BA populations also varied) This is a plausible scenario when you consider a hilly/mountainous habitat for such HG-rich populations, differing from the EEF crowd on the Alfold plain and such.
About Koros_HG:
-Sure, but it's likely that people like him contributed to later Chl and EBA populations of the Carpathians. Where else is the massive proper WHG in Jag and Mako_1502 from? And given him being an outlier, again, I'd venture to say that he was from the hill zone. Different phytogeographic zone from the LBK and their successors. This kind of thing can and often does correspond with different ancestral profiles.
-Now, as far as nothing like him appearing afterwards--again, not to belabor things, but we have exactly 0 samples from the mountains and hills. Let's sample Transylvania, Beskids, etc. and then see. It's a question of archaeogenetic visibility.
-But, alas, we actually DO have something similar afterwards from the Circum-Carpathian zone---from Urziceni in Romania. circa 3500 BC, Wallachian plain. And, yet again, such an individual appears to be an outlier amongst the standard EEF crowd. It seems to be of mediocre coverage, but appears mostly WHG, albeit with some unequivocal "balto-slavic" HG as well.
Scratch that a bit----the date is correct, but not Urziceni---it's Gura Baciului, which is Transylvania. A piedmontese setting which needs more sampling. :-) So, n=1.
I don't wanna make too many assumptions, but *IF* that sample is indicative of mainly WHG that far West in the chain, we're prolly better off sampling the Beskids for the elusive "Baltic" HG.
the "proper WHG" in BA Pannonians is also mostly inherited from the "mystery Hunter Gatherers". Baltic_BA carries some "proper WHG" as well.
when we get samples of the "mystery HGs", they will also be modelled with some proper WHG + minor EHG and EEF + a high distance. most of this distance being their specific drift.
I think when we get these samples, they will cover most of the HG ancestry in both Pannonians and Baltic_BA.
Gura Baciului is different. It really does seem to have ancestry from both "Mystery HGs" and Iron_Gates. But it looks like a dead end, because it has too little "Mystery HG" to be ancestral to either the Pannonians or Baltic_BA.
HGm,0.1320342,0.138722,0.1437584,0.1203498,0.096325,0.0338026,0.0172488,0.0233074,0.0511714,0.0007658,-0.0086068,-0.037587,0.0485814,0.046132,-0.0456568,0.0120654,0.0209648,-0.0079062,-0.0023638,0.0238856,0.0268268,0.009991,-0.0224304,-0.0764446,0.0007424
Using HUN_MBA_Vatya_o I made another HG ghost sample HGv:
HGv,0.1354497,0.1325265,0.1354805,0.1275042,0.092017,0.0412062,0.0194478,0.0237102,0.0522052,-0.0006828,0.0066982,-0.0344308,0.0434835,0.0824353,-0.0465178,0.003977,-0.0076933,0.024229,0.0098988,-0.0022205,0.023958,-0.0065528,-0.0362048,-0.1866228,0.0226932
HGm and HGv are good for modeling Corded_Ware_Baltic:Spiginas2
Target: Corded_Ware_Baltic:Spiginas2
Distance: 2.4249% / 0.02424892
28.8 HGm
17.6 UKR_Meso:I1763
14.8 RUS_Fatyanovo_Ivanovo_BA:MIL001
12.6 RUS_Fatyanovo_Yaroslavl_BA:NIK007
9.0 HGv
8.8 RUS_Fatyanovo_Yaroslavl_BA:NIK004
5.4 Corded_Ware_CZE_early:VLI076
3.0 Corded_Ware_DEU:I1538
The Baltic_BA is not so good:
https://postimg.cc/BLNXScSV
“EastPole, Baltic BA gives bad fit, because apart from this especial HG, it also contains the usual WHG from another source.”
But I have the usual WHG in my source data. It is not selected.
Target: Baltic_aLTU_BA:Turlojiske3
Distance: 3.4414% / 0.03441414
29.2 Corded_Ware_CZE_early:VLI007.merged
24.6 HGm
18.4 RUS_Fatyanovo_Ivanovo_BA:MIL001
10.2 CZE_EBA_Unetice:I14192
7.4 Yamnaya_RUS_Kalmykia:RISE546
5.2 HGv
5.0 Corded_Ware_DEU:I1538
Target: Baltic_LTU_BA:Turlojiske1
Distance: 3.5411% / 0.03541069
23.2 HGm
17.8 Yamnaya_RUS_Kalmykia:RISE546
15.4 RUS_Fatyanovo_Ivanovo_BA:MIL001
12.8 HGv
10.6 Corded_Ware_CZE_late:VLI010.A0101
7.4 Corded_Ware_DEU:I1539
6.4 Corded_Ware_CZE_early:VLI007.merged
2.8 Corded_Ware_DEU:I1534
2.0 Yamnaya_RUS_Caucasus:ZO2002
1.6 Corded_Ware_DEU:I1538
Target: Corded_Ware_Baltic:Spiginas2
Distance: 2.4052% / 0.02405177
31.2 HGm
17.2 UKR_Meso:I1763
15.2 RUS_Fatyanovo_Ivanovo_BA:MIL001
10.0 RUS_Fatyanovo_Yaroslavl_BA:NIK004
9.6 RUS_Fatyanovo_Yaroslavl_BA:NIK007
8.8 Yamnaya_RUS_Samara:I0443
7.8 HGv
0.2 Corded_Ware_DEU:I1538
I do agree that the Mystery_HG----defined as the non-CWC component of Baltic_BA----does contain a proportion of proper WHG in addition to highly drifted/divergent para-WHG stuff. But again, what you're seeing in the Jag model above(as well as a handful of other individuals) is separate. If this was truly an artifact and just an overfit for the Mystery_HG, you would not see free CWC hanging around like that, as it would be "eaten" by the Baltic_BA. I can see it being artifactual if we only got ~1-2% extra WHG and there was no significant change in the fit distance, but not the case here.
So, this leads me to think that G.Baciului-rich groups did also contribute in the long run to our Pannonian BAs, not just Mystery_HGs.
Honestly, it's likely that mixed/clinal groups consisting of Mystery_HG and GB-like ancestry in roughly equal measure were the most common south of the Carpathians. Hence, we see such frequent(but not invariable!) co-scoring of these ancestries. Perhaps on the Polish-facing slopes, they were mainly just Mystery_HG. But again, we won't really be able to infer with precision unless we actually get samples from piedmont and highland settings. It's very hard for me to see communities of such populations on the Hungarian plain during Copper and Eneolithic. Lowlanders=Baden-like agriculturalists imho.
"Let's keep this to ourselves, but word is that the mystery hunter-gatherer ancestry in the Kisapostag/Encrusted Pottery pops might be from a very late forager enclave in eastern Romania near the Black Sea coast"
The lolalization of the later source of this especial HG would be similar to the earlier one indicated by Daniel Gerber.
This Romanian group will be the ultimate proof that HG populations survived till the recent times in an unadmixed form but it wasn't the source of the "Balto-Slavic drift".
They were found almost at the mouth of the Danube.
@ambron
I don't know. There are tons of unpublished data (Reich Lab recently published samples with IDs over 30000) so maybe they have something like that already. What I know is that these Romanian hunter-gatherers can't be the source of the WHG-like ancestry in Baltic_BA.
The Baltic BA is on PCA more shifted towards HG than Bk-II, even though it contains less especial HG responsible for the Balto-Slavic drift. The addition of some other HG from another source is probably responsible for it. Maybe Daniel or Arza will explain it to us.
I want to point out that it appears in Eastern Hungary, too. Northeast, to be exact. Notable examples include Mako 1502 and 2 Fuzesabony samples. It also seems to persist into the Iron Age, although this fact in itself may belie more complex migratory/replacement dynamics. Eastern Hungary is notably undersampled in relation to the west, and, with further sampling, I think we would also see such a group level signal there in certain contexts and communities. The truth is, the Pannoanian basin was not a monolith in the BA, but more like a checkerboard with different groups seemingly situated in close geographic proximity.
Consider also that Encrusted Ware’s genesis is supposed to be in the north of the country, before its spread south and subsequent disappearance of the “Balto-Slavic” signal there(MBA Croatia lacks this signal)..
baltic_BA_HG,0.145865778629349,0.138086828145436,0.205810926968349,0.190088886398117,0.150478585247188,0.070200896730317,0.038713850614701,0.059386129060947,0.046820699816898,-0.074477607350249,-0.002962237352864,-0.052379350091551,0.106468345226262,0.133107862333246,-0.07567304308135,-0.0105677609469,0.019538569238818,-0.000371474417996,-0.004278398221292,-0.000979336594298,0.002908411535443,-0.019574860816113,0.015895731545906,-0.06706486147005,0.013425851948731
this is Baltic_BA with the steppe and eef removed. With these coordinates Pannonians can be modeled with perfect distances, and they all pick up some Iron Gates HG on top of this HG.
So it does look like the Pannonians went trough a step of absorbing Iron_Gates ancestry before coming to Pannonia, it makes sense because we know that there were still Iron Gates-rich populations in the region, like the ROU_C_o.
However, I still believe BA Pannonians all originate from a small group which had a massive founder effect. And the differences in the type of WHG are due to the intra-group variation, and their mixing with various eef and stepep groups which also carrried different types of WHG.
from Western Hungary there were practically no BA/IA samples until the recent Celtic study, and these Encrusted pottery which are about to be published. And it looks like here the WHG-rich Pannonians fared much worse troughout the BA/IA and were almost completely replaced by Celtic-related people at one point.
“this is Baltic_BA with the steppe and eef removed”
How did you do it?
then in Excel I subtracted Yamnaya from each coordinate, with the formula
(Baltic_Ba_coordinate- 0.46*Yamnaya_coordinate) / 0.54
Then I modelled the resulting coordinates with vahaduo, now they scored no steppe, only Iron_Gates and Barcin. Then I removed the Barcin from these coordinates the same way.
are you aware of the samples HUN_MBA_Vatya_o RISE479 from AllentoftNature2015,
and HUN_EIA_Prescythian_Mezocsat_o1 I18241 from Patterson 2021, and how do they compare to the new Encrusted Pottery samples?
because these are the most WHG-rich of the available Pannonian samples, and this PCA from Szeczenyi-Nagy's presentation shows that samples from "Hungary_EBA_MBA2", Serbia_IronGates_BA and Croatia_EBA have even more WHG than RISE479:
https://imgur.com/Ovs9FDG
from this it looks like these hunter gatherers passed trough the Iron Gates into Serbia and Croatia, and then north to Hungary, the Encrusted pottery samples being one of their early northern offshoots.
does your data suggest a different direction of the migration?
I just noticed you did something similar for Mezocsat and Vatya, could you share your methodology?
I was looking for HG populations which when mixed with Mezocsat and Vatya would produce Mezocsat_o1 and Vatya_o.
Using G25 coordinates and averages for Mezocsat and Vatya I calculated in Excel HGm and HGv coordinates using following formulas:
0.5*(HUN_EIA_Prescythian_Mezocsat + HGm) = HUN_EIA_Prescythian_Mezocsat_o1
0.5*(HUN_MBA_Vatya + HGv) = HUN_MBA_Vatya_o
I am thinking what HG pops would survive for such a long time and have such influence on others. I guess it had to be quite populous. Maybe a Mesolithic pop which switched to farming early like Bug-Dniester culture?
https://imgur.com/a/E67Vptr
I wonder how your HG ghost compares to one I made earlier. Not near my files right now, but I had a similar approach except that I used a more proximal source to get the "ballpark" modeling of Baltic_BA, as opposed to Yamnaya+Barcin. So, I used a Corded Ware average comprised of PCW and Fatyanovo-like CWC and subtracted this from Baltic_BA. Again, operating on the assumption that "standard" CWCs picked up this cryptic HG from a prolonged stay near the northern Carpathian foothills. In your case, you seem to favor (an early) admixture event of early CWC(or Yamnaya) profiles with Cryptic HGs. Naturally, your ghost has a higher content of WHG proper and EEF.
Regarding it being a founder effect and intragroup variation: that is of course possible, definitely. We just won't know for sure the dominant flow of things until we can get more mountain samples, imo.
Do bear in mind, though, that there are at least two types of BA Pannonians, and this is best seen in the Mokrin set. Some are just "steppe"+EEF balanced mixes, whereas others definitely show the strong Cryptic shift. Given the heterogeneity of the Mokrin set, a high degree of mobility is inferred.
So, if I understand, you basically suggest the following sequence: Baltic_BA-like folk(already harboring cryptic HG) penetrate into Pannonia. While there, they absorb some Rou_C_o-rich populations and also mix with EEF+steppe mixes(who also potentially harbor some Rou_C_o admixture).
My scenario involves steppe-rich groups(CWC or otherwise) moving into Pannonia without any HG tacked on. While there, some absorb varying degrees of Cryptic_HG+WHG from the hillier refuge zones, whilst others mainly absorb Baden-like. Over time, these two profiles mingle and create tertiary mixes in places in this highly-mobile context.
And, I definitely echo what you say about eastern Hungary. "Celtoid" admixture does seem to be important in attenuating Encrusteds' profile in the West. But I also think there was some flow from the Balkans and/or surge in EEF-steppe BA Pannonians(in regards to Hrv MBA/EIA).
I don't think anything Baltic_BA-like was involved in Hungary. I think Usatovo was highly drifted and WHG-rich (maybe something like 70%), maybe with some minor eef and steppe.
They were pushed by the Yamnaya expansion, and moved west trough Romania, mixing with ROU_C (eef-rich), ROU_C_o (IronGates_HG-rich), and finally with Yamnaya too. And by the time they reached Hungary, they were already complex mixes like the "Mako" sample.
Then around 2000 BC a mix of CWC and remnants of pure Usatovo (without the extra IronGates, eef, etc.) somehow appeared in the Baltic.
altvred from Anthrogenica ran DATES analyses which show that Mako and Spiginas2 are both a result of a very recent Steppe+WHG mix, we are looking in both cases at members of young populations which had just formed.
the Iron Age Mezocsat outlier turned out to be a very old mix, dating back to the Mako period, which confirms this method.
I tried with IronGates and Yamnaya because they both have a slight BS affinity, and I was hoping they would cancel each other and none would get inflated.
I'm very satisfied with the resulting ghosts. On a PCA like this, they plot together with WHG/EHG groups, meaning I've succesfully extracted the Steppe/EEF from them, and I didn't remove too much either (in that case they would plot in the empty space, away from both WHG/EHG, Steppe and EEF)
https://i.imgur.com/SOntbsC.png
Thanks for the response, it didn't occur to me that Encrusted Pottery could be the core population from which this WHG admixture spread, but now that you pointed it out, it does make sense.
Now it remains to see the exact location and dating, autosomes and uniparentals, and archaeological context of those unpublished samples from Szécsényi-Nagy, to see how exactly they relate to the Encrusted Pottery population.
Hope all is well with you. Things are quiet on ancient dna at the moment but thought I might point you to this as might be one to watch for future - https://www.ucl.ac.uk/biosciences/news/2022/mar/congratulations-dr-sam-morris
"Sam Morris was awarded his PhD (as part of the BBSRC LiDO DTP) for his thesis on "Harnessing haplotype sharing information from low coverage sequencing and sparsely genotyped data". "
"Thesis abstract: The proliferation of DNA from ancient remains is revolutionising the understanding of past population structure and demography. However, these data are often sparse (<1x coverage), making it challenging to extract reliable haplotype information from them, i.e. to model associations among linked SNPs. While this may not be essential when inferring population sub-structure involving genetically diverged groups, larger cohorts of samples from geographically proximate regions are emerging. In such cases, subtle genetic differences may be captured with haplotype information, demonstrated in analyses of cohorts containing geographically nearby present-day individuals.
Among such haplotype-based methods, Chromopainter has been used extensively in ancient DNA papers that analyse higher coverage (>1x) samples. Lower coverage data can be imputed to provide the dense SNPs that haplotype-based techniques require. However, imputation typically uses modern reference panels, and may be sensitive to effects that obscure fine-scale ancestry signals. Although efforts have been made, there has yet to be a detailed characterisation of the effect of imputation bias on Chromopainter analysis of a range of available aDNA populations for different coverages, and whether more power can be gained with new techniques.
In this thesis I propose modifications to the Chromopainter method to assist extracting haplotype information from low-coverage samples. These include accounting for allele probabilities, retaining SNPs adhering to specific criteria, and upweighting the likelihood contribution of genomic regions containing higher coverage SNPs. I explore these in the context of detecting subtle population structure, including measuring the loss in haplotype information from subsetting data to SNPs that overlap among SNP arrays.
I use these insights to analyse two datasets of newly sequenced ancient samples from Bavaria and Slavic-speaking regions."
https://www.cell.com/cell/fulltext/S0092-8674(22)00267-7
I would be more cautious in using the term “genetic continuity”. In terms of macro-components? Sure. But it doesn’t at all preclude large population turnover mediated by a genetically similar population.
Iron Age Hungary had a population harboring a “Baltic-BA-like” component of ancestry. But it doesn’t mean that Hungarians more or less descend from them in situ. In fact, even the Roman/late Roman record shows that Hungary was already a checkerboard with ancestry from the south(Balkans) and Germanic zones coming in. And then, as we all know, the Slavs come in a massive way.
Point is, most of the Baltic_BA is from the new Pannonian Slavs+later Polish, Slovak, and Serb infusions. Not from those Iron Age locals. In fact, I think those early modern Slovaks/Poles and Serbs had more a contribution than people realize.
Target: Hungarian
Distance: 2.6629% / 0.02662937
82.6 Scythian_HUN
17.4 French_Nord
0.0 ITA_Collegno_MA_o1
Target: Hungarian
Distance: 0.7784% / 0.00778400
52.6 Polesia
37.4 French_Nord
10.0 ITA_Collegno_MA_o1
0.0 Scythian_HUN