Hello authors, Thanks for the interesting preprint and data. However, I'd like to see you address a couple of technical issues and perhaps one theoretical issue in the final manuscript: - the output you posted shows some unusual results, which are potentially false positives that appear to be concentrated among the shotgun and noUDG samples. I'm guessing that this is due to the same types of ancient DNA damage creating IBD-like patterns in these samples. If so, isn't there a risk that many or even most of the individuals in your analysis are affected by this problem to some degree, which might be skewing your estimates of genealogical relatedness between them? - many individuals from groups that have experienced founder effects, such as Ashkenazi Jews, appear to be close genetic cousins, even though they're not genealogical cousins. Basically, the reason for this is reduced haplotype diversity in such populations. Have you considered the possibility that at least some of the close relationships that you're seeing between individuals and populations might be exaggerated by founder effects? - thanks to ancient DNA we've learned that the Yamnaya phenomenon isn't just an archeological horizon, but also a closely related and genetically very similar group of people. Indeed, in my mind, ancient DNA has helped to redefine the Yamnaya concept, with Y-chromosome haplogroup R1b-Z2103 now being one of the key traits of the Yamnaya identity. So considering that the Corded Ware people are not rich in R1b-Z2103, and even the earliest Corded Ware individuals are somewhat different from the Yamnaya people in terms of genome-wide genetic structure, it doesn't seem right to keep claiming that the Corded Ware population is derived from Yamnaya. I can't see anything in your IBD data that would preclude the idea that the Corded Ware and Yamnaya peoples were different populations derived from the same as yet unsampled pre-Yamnaya/post-Sredny steppe group.See also... Dear Harald #2 On the origin of the Corded Ware people
Saturday, April 8, 2023
Dear Harald...
I've started analyzing the Identity-by-Descent (IBD) data from the recent Ringbauer et al. preprint (see here). Unfortunately, it'll take me a few weeks to do this properly, so I won't be able to write anything detailed on the topic for a while.
Meantime, this is the comment that I left for the authors at bioRxiv (at this time it's still being approved, but it should appear there within a day or so, possibly along with a reply from the authors):
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443 comments:
«Oldest ‹Older 401 – 443 of 443"Mittani is unrelated to Sintashta from what we have, but not Indians"
(=but Indians aren't unrelated to Sintashta)
@Vara @Copper Axe
I've had similar issues. Try limiting comment length to 2500-3000 characters tops (despite the 4000 limit) and avoid too many paragraphs. Worked for me
@Orpheus
I love how you guys claim Sintashta is unrelated to Indo-Aryans and modern Indians because their Y-DNA just matches Indians in 2500 B.C (talking about R1a-L657) and not later but folks from Hasanlu, BMAC, Shar-I-Sokhta, KGZ_BA or Post-BMAC (Sappali Tepe,..) are definitely closer because their J2, R2, L1 or G clades match South Asians in 4.000-10.000 B.C (often even before) lol. If anything Sintashta is the Brone Age culture today from which we have Y-DNA closest to modern Indians. I mean find me a high coverage J2, R2, G or L1 sample from Iran, BMAC or South Central Asia from the Bronze Age/Iron Age that has a Y-DNA match to South Asians closer than Sintashta. Even much if not all of the Swat_IA non-steppe Y-DNA is much more distant to most Indians outside North Pakistan/Punjab than Sintashta
@Coldmountains "you guys"
Take your meds
"unrelated to Indo-Aryans and modern Indians"
I fixed my position on Sintashta not being related to modern Indians since it was based on a non-sequitur. I don't have preconceived positions, so I assume you're not referring to me here.
The issue here is the extent of relation and the timeline/source of relation to early Indo-Iranian speakers (or/and culture-wise wrt Avestan/Vedic) for the Indo-Iranian origin argument. Secondary arguments with relation to Indo-Aryan only, can also be made as I mentioned earlier. Sintashta not being an origin doesn't mean they necessarily weren't a vector.
Not sure what your argument is
@Orpheus
You don't have any arguments.
Everything you're claiming is based on your lack of understanding of the data.
It seems like there's been a drought of big (or even medium-sized) aDNA papers lately. Hopefully something consequential will be forthcoming. I'm a little surprised the Danubian limes paper hasn't been finalized and printed yet.
I'm still trying to catch up with all of the new papers and samples that came out over the last six months.
Hopefully things stay quiet for a while until I'm done.
Off topic: Was this published and I've forgotten about it?
https://iris.uniroma1.it/handle/11573/1679178 - "History and evolution of the Picene Culture through Ancient DNA analysis" - "Abstract: Until the Roman conquest, the Italian peninsula was characterized by the presence of many different ethnic groups. Although considerable archaeological research has been conducted, several aspects of the origins and evolution of these ancient populations are still unknown. We focused our attention on the Picenes, a civilization established in IX-III cc. BCE on the Adriatic coast of central Italy that, on the basis of archaeological data, seems to be composed of many local groups not necessarily ancestrally related. During the Iron Age, central-eastern Italy experienced the full development of the Picene culture, but in the early years of the III c. BCE Picenes underwent Roman expansion and the whole region was subject to Rome. In order to investigate the origin of the Picenes and the genetic legacy of the Roman conquest, we performed the ancient DNA analysis of new samples from different burial sites of central Italy. On the basis of the material culture, the selected sites belong either to Picenes or to other pre-Roman and Roman cultures. We then framed our data in the context of published Italian and European ancient data, for a total of more than 1500 samples included in our study. Our preliminary results show that the genetic diversity of Picenes seems to be consistent with other Iron Age Italian and European people, suggesting a genetic continuity with previous central Italian cultures. On the other hand, during the Roman rule there was a shift in the genetic landscape of central Italy possibly due to an influence from eastern Mediterranean people. "
That paper on Picenes seems also have a rephrased abstract from 2022: https://iris.uniroma1.it/handle/11573/1679177 - "Archaeogenetics of the Picenes and the legacy of the Roman expansion in Central Italy" - "Abstract: Until the Roman conquest, the Italian peninsula was characterized by the presence of many different ethnic groups. Although considerable archaeological research has been conducted, several aspects of the evolution of these ancient populations are still unknown. We focused our attention on the Picenes, a civilization established during the Iron Age on the Adriatic coast of Central Italy. They flourished until the beginning of the III century BCE, when their territory was conquered by Romans. To investigate the origin of the Picenes and the genetic legacy of the Roman conquest, we extracted DNA from 91 ancient individuals belonging to four different Central Italian burial sites (two Picene, an Etruscan and a Roman Imperial time necropolises) to frame the genetic variability of the Picenes in the local context. Our preliminary results show no major genetic differences between Picenes and other contemporary populations like the Etruscans, suggesting a shared ancestry for the Iron Age Central Italian populations. Nevertheless, Picenes show some additional genetic influences, possibly linked to other European cultures. Similarly to other areas of Central Italy, the arrival of the Romans caused a partial shift in the genetic landscape of the region towards Near Eastern and North African components, although some continuity between the Iron Age and the Imperial time is still present. "
@Davidski
Not sure how useful it may be to you, but this is a more or less updated list of the G25 coordinates you have released but haven't added to the Ancients spreadsheet.
https://www.dropbox.com/s/d9zhf0fzaukmsat/G25%20Ancients%20not%20on%20the%20Spreadsheet.txt
Hello, could you do this sample of Dzudzuana2? https://www.mediafire.com/file/88gu7bnrdur2zhb/S2949.zip/file
@Davidski
This thread has a lot of the missing samples, in case you missed any and want to look.
Thanks
https://anthrogenica.com/showthread.php?28091-List-of-G25-ancient-samples-not-on-Davidski-s-spreadsheet
@ Huck Finn
'' my opinion the Ymyakhtakh expansion is a parallel expansion vs. the early Uralic one. That being said, it is far from certain that the language of this N-rich group was Uralic already at that stage.''
Parallel to what ?
Looking to your sources on Lame-O-Genica, we have to engage in a special pleading scenario that FU actually arose near the Urals just because a couple of outmoded linguists are too embarrased to admit their models are not viable in anthropological terms, and we even have to re-invent the FU tree to fit in this model.
I thought this was already settled when Sam put Ryukendo in his place about BOO.
And then there's the customary cliches about how 'genes dont speak languages' and that archaeology has no bearing on linguistics from the comedians who think that proto-Germanic arose specifically in northeastern Sweden "because Finninc loans".
Not particularly enthralling.
@ Rob: Ymyakhtakh apparently did not speak anything related to Uralic. However because of the loan words into Yukaghir, early Uralic was, at some point of time at least and for some time, possibly spoken near early Yukaghir. The other option is that those are later loans from Samoyedic into Yukaghir.
@Norfern
Scaled
GEO_Dzudzuana_UP:S2949,0.062603,0.099522,-0.009428,-0.002261,0.029852,-0.017012,0.001175,-0.001846,0.03211,0.02606,0.007632,-0.011989,0.001635,0.012799,0.000271,-0.003182,-0.01343,0.004687,-0.007416,0.003377,0.026453,0.007172,-0.01479,-0.029281,-0.00012
Raw
GEO_Dzudzuana_UP:S2949,0.0055,0.0098,-0.0025,-0.0007,0.0097,-0.0061,0.0005,-0.0008,0.0157,0.0143,0.0047,-0.008,0.0011,0.0093,0.0002,-0.0024,-0.0103,0.0037,-0.0059,0.0027,0.0212,0.0058,-0.012,-0.0243,-0.0001
@Davidski
Thank you! This should be okay now and I think if the plink files corroborate qpgraph and f4 results, this is finally Dzudzuana. After all these years.
@ Huck
''Ymyakhtakh apparently did not speak anything related to Uralic."'
LOL How is that at all apparent ? Are we to believe that this significant migration somehow brought across northeastern Europe and all the way to Finland a language "completely unrelated to uralic', and then FU in fact arrived via some ghostly migrations that left no trace ?
I don't think one needs to deliver much furhter arguementation at this stage.
The rest of the observed phenomena relates to later languaegs shifts due to expansion of Tungus and Turkic languages (e.g. Avars), which eroded the original early FU language base in north-central Siberia.
It seems like on G25 the Dzudzuana has the same qualities as other West Eurasian UP samples but more southern - https://imgur.com/a/qGqgSon
Has a West Eurasian affinity, lacks either high genetic drifts that happened in the LGM, or has some genetic drift that otherwise isn't well represented by modern people, and therefore ends up compressed into the middle of G25 dimensions representing modern variation. (Which means some compression towards present day groups that represent the most admixture between post-LGM Eurasian groups, such as certain South Asian groups).
This sample has very little to do with the much later Anatolian farmers.
@Matt Does this Dzudzuana sample have any hits on the snps involved with pgmentation? Any for eye color, skin color and etc?
@Norfern
May I know where you got the Dzu2 sample from? Doi or link?
G25 isnt good for deep ancestry given the high non shared drift. But still, here's a go. crazy 25% distance though.
Target: IRN_Ganj_Dareh_N
Distance: 25.1370% / 0.25137028
37.0 RUS_MA1
35.4 GEO_Dzudzuana_UP
20.0 Levant_Natufian_EpiP
5.4 IND_Great_Andamanese_100BP
2.2 ETH_Mota
0.0 ITA_Villabruna
0.0 MAR_Taforalt
0.0 RUS_AfontovaGora3
0.0 RUS_Kostenki14
0.0 RUS_Shamanka_EBA
0.0 RUS_Shamanka_N
0.0 RUS_Sidelkino_HG
0.0 TUR_Pinarbasi_HG
Target: GEO_CHG
Distance: 24.5142% / 0.24514152
71.8 GEO_Dzudzuana_UP
28.2 RUS_MA1
0.0 ETH_Mota
0.0 IND_Great_Andamanese_100BP
0.0 ITA_Villabruna
0.0 Levant_Natufian_EpiP
0.0 MAR_Taforalt
0.0 RUS_AfontovaGora3
0.0 RUS_Kostenki14
0.0 RUS_Shamanka_EBA
0.0 RUS_Shamanka_N
0.0 RUS_Sidelkino_HG
0.0 TUR_Pinarbasi_HG
Hello David,
I was wondering if you have G25 coords for these two samples from Central Ukraine which seem to be Western Sredny Stog variants.
ukr104 (Deriivka II, ~3500 BC)
https://assets.researchsquare.com/fi...f?c=1662993174
SSX (Kolomiytsiv Yar Tract, ~3900 BC)
I'm pretty sure both are wamen, so no Y-DNA. SSX is in Trypillian territory but is genetically unrelated to Trypillians, and isotope analysis reveals it likely was some migrant from nearby Sredny Stog peoples. Ukr104 is late, maybe post Sredny Stog proper, but is identified as archaeologically belonging to Sredny Stog.
I got it from this paper https://www.biorxiv.org/content/10.1101/2022.01.13.476259v1
The repository has been out for a while
https://www.ebi.ac.uk/ena/browser/view/PRJEB54983
@WSH
Your link is broken.
Iran probably has some BachoKiro IUP stuff in it that won’t show with G25 based calcs
the Dzu Dzu boo boo is just a local group which went extinct during the LGM. It has no direct bearing on either WHG or farmers
Dzudzu probably represents a population from UP Anatolia that eventually contributed to the formation of CHG.
So like I said before, Dzudzu isn't the majority base of the West Eurasian gene pool, but it and its close relatives did contributed to various populations, especially Anatolian Neolithic farmers.
@Modas Califa, I only what you know from Lazaridis preprint, and I don't think they had any hits on the relevant pigmentation SNPs.
It seems like those variants are not quite sweeping around until later than Dzudzuana (i.e. they're not universal in even the Pinarbasi HG from 15kya), so I'd be surprised if Dzu at such an early time had any derived depigmentation variants.
I think the published dna that Norfern accessed this from has ultra-low coverage of 7513 SNPs (of a max 1240000 SNPs), so that seems good enough to get an impression on G25 but unlikely to give good coverage to pigmentation variants (also may be shakier in the precise position within the 25 dimensions than a good coverage sample would be).
@ Davidski
''Dzudzu probably represents a population from UP Anatolia that eventually contributed to the formation of CHG.''
Im sure it or a population similar to it contributed to CHG, but the issue of AHG is a puzzle because there are no sites in Anatolia which can be dated before 25,000 calBP. And I think its fairly clear that AHGs come from Europe as populations retreated south during the Ice Age.
''Dzudzu isn't the majority base of the West Eurasian gene pool, but it and its close relatives did contributed to various populations, especially Anatolian Neolithic farmers.''
Dzudzu isn;t the clade they make it out to be. Its too young, and i'd be it comes out to be a mixture of Kostenki-like and Zlaty Kun. Given that such populations were already widespread by 35,000 calBP, the claims in the preprint seem hyperbolic.
@Matt @Rob @Huck Finn Ymyakhtakh is probably ancestral to all these Paleo-Siberian relic tribes which are grouped together under the umbrella term “Paleo-Siberian”, predating Uralic and Transeurasian (read “Altaic”) groups which are referred to as “Neo-Siberians”. They are something on a clade of ANE and ENA or ANA (East Asian or Notheast Asian).
@Rob
I do not believe that the mixture that gave rise to Dzudzuana contains Zlaty Kun, as Dzudzuana is significantly farther from East Eurasians than Paleolithic/Mesolithic Europeans, farther even than Kostenki 14. On the other hand, Zlaty Kun is equally distant from Paleolithic Europeans and East Eurasians, and perhaps a little closer to East Eurasians.
That Basal-Eurasian fraction that Lazaridis concluded to be in Dzudzuana does not appear to be Zlaty Kun.
@Davidski
Oops, my bad.
KYT Paper: https://www.biorxiv.org/content/10.1101/2022.10.31.514526v1.full
ukr104 Paper: https://europepmc.org/article/ppr/ppr543294
As a sanity check, ZK belongs to mtDna N, a west Asian farmer lineage
@ Andrze
Ymkht is deeply very East Asian
This erodes any notion of FU being an ANE related language as well as the final nail in the coffin for Indo-Uralic
The two languages are almost polar opposites as far as geography goes
Dene-Yeneseain seems to represent an ANE rich group
There is no genetic paleo-Siberian, it’s just a language area
@ Modas
''I do not believe that the mixture that gave rise to Dzudzuana contains Zlaty Kun, as Dzudzuana is significantly farther from East Eurasians than Paleolithic/Mesolithic Europeans, farther even than Kostenki 14. On the other hand, Zlaty Kun is equally distant from Paleolithic Europeans and East Eurasians, and perhaps a little closer to East Eurasians.
That Basal-Eurasian fraction that Lazaridis concluded to be in Dzudzuana does not appear to be Zlaty Kun''
Your error is that you have taken 'F3-stat riddles' (A is closer to B, etc) which are preliminary forms of interrogation and created a false novella.
If we were to make this error, we'd still think Bacho Kiro is 'east Asian', as a some people did, when the preliminary genotypes were released.
We would also believe that post-40K Europeans have nothing to do with BK, but all of them (outside the east European plain) have such admixture incl WHG / Tagliente.
You're also incorrect about ZK. Anyone capable of using qpGraph can discern that it is a reasonable proxy for some form of 'basal', not that I think it is a useful concept anymore.
And the the fact she has mtDNA N - a lineage found in Neolithic West Asians, only re-affirms this observation.
So we'll see what Dzudzuana & the older Satsurblia turn out to be, but some form of 'west Eurasian' and 'basal' mix is the most likely scenario. And such mix was already around western Eurasia by 35,000 calBP at the latest.
@Rob
If we were to make this error, we'd still think Bacho Kiro is 'east Asian', as a some people did, when the preliminary genotypes were released.
We would also believe that post-40K Europeans have nothing to do with BK, but all of them (outside the east European plain) have such admixture incl WHG / Tagliente.
Is Bacho Kiro not East Asian? I used to think not, but apparently its neanderthal segments are more similar to those of modern East Asians than modern West Eurasians. It also does seem to be slightly more related to East Asians than pre-basal West Eurasians.
I mean, obviously it isn't "East Asian" but you know what I mean.
@ WSH
I suspect it is "Iranian", so eastern West Asia, that's were the 'hub' probably was.
@WSH
I don't have those samples.
@Rob
I suspect it is "Iranian", so eastern West Asia, that's were the 'hub' probably was.
I'm not sure I am following here. What do you mean by the hub?
@Davidski
That's a shame
Hello,
Somewhat off topic but @Davidski would it possible to convert this sample to G25 coordinates?
https://www.nature.com/articles/s41559-023-01987-0
23k year old individual from Spain.
@Rob, Huck Finn
"Exactly, it seems that the common genetic root of the Uralic speakers was coming from some place much further east. I'm toying with an idea that the root can fex be connected to the area between Hulunbuir and Tsita. Vitim river nearby connects the area with Lena river, which would quite nicely explain the Ymyakhtakh connection, however in my opinion the Ymyakhtakh expansion is a parallel expansion vs. the early Uralic one. That being said, it is far from certain that the language of this N-rich group was Uralic already at that stage."
The area Huck Finn described is on the eastern Eurasian steppe. There is no contradiction in a Far Eastern homeland for Uralic and the Indo-Uralic hypothesis since late Proto-Indo-European may have been spoken by Afanasievo as far East as Central Mongolia.
@ WSH
Sorry just slang, i.e. a geographic refuge for out of Eurasia populations, at least one branch of them
@ Marlow
Ask anyone here - Afansievo came from Yamnaya groups in the western steppe likely the Dnieper-Don interfluvial
Hence as I suggested, quite the opposite side of things.
I thought I'd just post this paper in case anyone hasn't seen it yet:
https://www.nature.com/articles/s41586-023-06055-y#citeas
I find it really fascinating. The paper suggests that modern human ancestry comes from two major "stem" groups who began to differentiate from one another 1 million years ago or more.
Neanderthals and Denisovans derive their ancestry exclusively from "stem 1" whereas all modern humans descend from both "stem 1" and "stem 2." West Africans also received an extra, late (LGM) pulse of "stem 2" ancestry.
In one of the models (the merger model), Khoi-San groups get ~70% of their ancestry from stem 2 and ~30% of their ancestry from stem 1, while East Africans and Eurasians get ~52% of their ancestry from stem 2 and ~48% from stem 1 (excluding later Neanderthal admixture).
Pretty mind blowing and lines up with some of Dienekes' thinking IMHO.
Did you see this:
https://tinyurl.com/4ak3fhn3
At the end, Alexey Nikitin says that possibly Yamnaya came from Trypillia culture, and that Nick Patterson, or David Reich will clarify it at the end of the year too.
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