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Thread: Basal Eurasian in 25,000 yo site?

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    Basal Eurasian in 25,000 yo site?

    Well, well, well, :) From the Pinhasi, Skoglund group, no less. 25,000 years old and from the Satsurbia Cave in the Caucasus,. I must say it's a surprise.

    See:
    https://www.biorxiv.org/content/10.1...#disqus_thread

    "Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

    Pere Gelabert, Susanna Sawyer, Anders Bergström, Thomas C. Collin, Tengiz Meshveliani, Anna Belfer-Cohen, David Lordkipanidze, Nino Jakeli, Zinovi Matskevich, Guy Bar-Oz, Daniel M. Fernandes, Olivia Cheronet, Kadir T. Özdoğan, Victoria Oberreiter, Robin N. M. Feeney, Mareike C. Stahlschmidt, Pontus Skoglund, Ron Pinhasi

    Summary

    Archaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the late Pleistocene genetic histories of these three species, and demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history.
    Highlights

    • We demonstrate for the first time that genome sequencing from sediments is comparable to that of skeletal remains
    • A single Pleistocene sediment sample from the Caucasus yielded three low-coverage mammalian ancient genomes
    • We show that sediment ancient DNA can reveal important aspects of the human and faunal past
    • Evidence of an uncharacterized human lineage from the Caucasus before the Last Glacial Maximum
    • ∼0.01-fold coverage wolf and bison genomes are both basal to present-day diversity, suggesting reshaping of population structure in both species


    This one is going to require very close reading of both the paper and the supplement.




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    "We find that the SAT29 sample clusters with the Dzudzuana2 individual and notwith the late Upper Paleolithic and Mesolithic genomes from the region, or with any ofthe other pre-LGM Eurasian genomes. Unsupervised ADMIXTURE clustering(Alexander and Lange, 2011) further supports a high similarity between SAT29 andDzudzuana2 (Figure 2B, Figure S2). "

    "SAT29 shares more driftwith Villabruna (Italy, 12140±70 bp) (Fu et al., 2016) and Dzudzuana2 than with otherancient individuals (Figure S3A), including the post-LGM individuals from the Caucasus(Satsurblia and Kotias). Among present-day Eurasian populations, SAT29 shows highergenetic affinity to Northern and Western Europeans rather than Central and SouthernAsians (Figure S3B)"

    "we recovered 4,953 humanmitochondrial DNA (mtDNA) reads, providing 15-fold coverage of the mtDNA. Theconsensus sequence has 16 derived positions (Table S3) compared to the rCRSsequence and belongs to haplogroup N like individual Dzudzuana3 from Dzudzuanacave (Figure 2C). We built a maximum parsimony (MP) tree with 68 ancient and 167modern human mt genomes (Table S4, Figure 2C). The SAT29 sequence is positionedon a branch together with BK-CC7-355 (42450 ± 510 ka) and BK-BB7-240 (41850 ±480 ka) from the Bacho-Kiro site in Bulgaria, the most ancient west-Eurasianmitochondrial sequences (Hublin et al., 2020) as well as Dzudzuana3 (Lazaridis et al.,2018)."

    "We estimate 1% Neanderthal ancestry in the SAT29 sample, although with largeuncertainty due to the low amount of data (95% confidence intervals: 0-6.6%). Thispoint estimate is similar to that of Dzuzuana2 and likely lower than that of PalaeolithicEuropeans due to dilution from Basal Eurasian ancestry (Lazaridis et al., 2018)Our results from the human genomic data from the SAT29 sample are thus consistentwith the study by Lazaridis et al (2018), revealing a a previously undocumentedpre-LGM human ancestry from the Caucasus that contributed to various succeeding Eurasian populations. The low coverage of the SAT29 genome, however, did not allowus to detect any differences in ancestry patterns between Dzuzuana2 and SAT29.

    What the hell? Why wasn't Lazaridis allowed to publish his Dzuzuana paper? Some idiot at the journal or his own LAB? Shame on whoever it was.

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    Some of the data in the Supplement is missing.

    Anyone have a graphic of the modern PCA which is both labeled and legible?

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    Yes, in fact many images are missing from the supplementary material referring to the figures.
    https://www.biorxiv.org/content/bior...?download=true

    It seems to me that the supplementary material for the tables is complete, I think.
    https://www.biorxiv.org/content/bior...?download=true

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    extremely interesting paper
    if it is true that in the caucasus
    there was some human remain who carry significant basal eurasian ancestery
    that it is a big kick in the head to the theory
    of y haplogroup E who might relate to basal ancestery
    phenotype:
    gracile- med

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    "a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe."

    Why 'parts of Europe'? Don't all Europeans have basal Eurasian ancestry?

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    I think they're talking about ancient peoples.

    I really wish they'd fix the figures part of the Supplement. It would answer some of my questions.

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    Quote Originally Posted by Philjames100 View Post
    "a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe."

    Why 'parts of Europe'? Don't all Europeans have basal Eurasian ancestry?
    I guess the El Miron cluster didn't.
    Maybe neither early EHG.

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    ENA: PRJEB41420

    I know it is a pre-print, so maybe that is why no results are coming up in the search. I can't wait to see these!

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    Quote Originally Posted by kingjohn View Post
    extremely interesting paper
    if it is true that in the caucasus
    there was some human remain who carry significant basal eurasian ancestery
    that it is a big kick in the head to the theory
    of y haplogroup E who might relate to basal ancestery
    Wouldn't say so. Isn't the estimate of higher Basal Eurasian mostly based on the insecure estimatation of Neandertal ancestry? And no yDNA retrieved, not that it could be decisive without larger samples taken.

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    don't you think it is more likely that y haplogroup E was connected to the ANA component
    than to basal eurasians


    p.s
    haplogroup E is extremely rare in caucasus ( some e-v13 cases in ossetians though)
    and yes SAT29 is a female remain ( so y haplogroup not relavant as you mention correctly)
    but in that earlier date that north with significant basal ancestery pretty cool ....
    her neaderthal is 1% acording to the paper
    and they assume the low % compare to other earlier ancient is connected
    to dilution by basal ancestery

    i myself score 1% neaderthal in geno2 next lol
    and it is lower than europeans because the avarege acording to them was 1.2%

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    Quote Originally Posted by kingjohn View Post
    don't you think it is more likely that y haplogroup E was connected to the ANA component
    than to basal eurasians


    p.s
    haplogroup E is extremely rare in caucasus ( some e-v13 cases in ossetians though)
    and yes SAT29 is a female remain ( so y haplogroup not relavant as you mention correctly)
    but in that earlier date that north with significant basal ancestery pretty cool ....
    her neaderthal is 1% acording to the paper
    and they assume the low % compare to other earlier ancient is connected
    to dilution by basal ancestery

    i myself score 1% neaderthal in geno2 next lol
    and it is lower than europeans because the avarege acording to them was 1.2%
    My Neandertal is, at least according to 23andme, above average.

    Concerning ANA vs. BEA and haplogroup E, nobody really knows, but I'd say that both were at some point predominated by haplogroup E most likely. BEA is best associated with E1b1b in the Near East. But we will see, especially with samples from the Levante, Southern Arabia and North Eastern Africa from the Paleolithic. Single samples prove little in this respect, unless there would be a BEA heavy early individual with E. But the absence is little proof for anything conclusive in this respect, especially since this individual is just, at best, and if at all, proof for BEA presence in the region that early. Nothing else.

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    Quote Originally Posted by Riverman View Post
    My Neandertal is, at least according to 23andme, above average.

    Concerning ANA vs. BEA and haplogroup E, nobody really knows, but I'd say that both were at some point predominated by haplogroup E most likely. BEA is best associated with E1b1b in the Near East. But we will see, especially with samples from the Levante, Southern Arabia and North Eastern Africa from the Paleolithic. Single samples prove little in this respect, unless there would be a BEA heavy early individual with E. But the absence is little proof for anything conclusive in this respect, especially since this individual is just, at best, and if at all, proof for BEA presence in the region that early. Nothing else.

    afcorse
    becuase you are full european i am not
    i am mixture of levantine+ south european with some east european genes ( from my bulgarian granny)

    the question:
    who do you think spread this basal ancestery that far north to the caucasus at that
    early date of the paleolithic
    and what y haplogroups you think this group carry
    ?

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    I highly doubt it was "E".

    Recent papers have shown that at the LGM people huddled in certain refuges. Drift could of course be part of why certain y lines predominate, and there might have been others around, but didn't the nearest refugia carry "G"?

    What was the closest refugia in India, and what y did they carry? Anyone know?

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    Quote Originally Posted by kingjohn View Post
    afcorse
    becuase you are full european i am not
    i am mixture of levantine+ south european with some east european genes ( from my bulgarian granny)
    I score higher Neandertal, on 23andme, than much more Northern people than me though.

    Quote Originally Posted by Angela View Post
    I highly doubt it was "E".

    Recent papers have shown that at the LGM people huddled in certain refuges. Drift could of course be part of why certain y lines predominate, and there might have been others around, but didn't the nearest refugia carry "G"?

    What was the closest refugia in India, and what y did they carry? Anyone know?
    We would like to know, but it isn't for sure yet. For sure is however that most of todays Indian haplogroups came later from West Eurasians and East Asians.

    Concerning Basal Eurasians, I agree on the refuge scenario, the issue however is that I would place BEA between North Eastern Africa (Nile Valley), Sinai, Levante, Southern Arabia originally. And I don't think that the main West Eurasian lineages were living there and dominating the BEA population. Since you mention G, I would suspect they intermixed early on and on a regular base with the main body of the BEA in the region described, so they could have entered the mix early on, which complicates the effort to trace it down. But the original haplogroup, I think there is practically no good alternative to E. Basal Eurasian was originally spread like Arabs are today imho and directly North of them lived the main/crown Eurasians, with which they intermixed fairly early and regularly. Within the BEA sphere I expect massive changes to have taken place and founder effects.

    Like if comparing Natufians and pre-Natufian Near Easterners with ANA, they are at the opposite ends of the evolutionary trends. ANA and later IBM were massive, hypermasculine and hypermorphic, extremely tall and robust people, the Near Easterners, even before the Natufians, were relatively shorter, more gracile, refined and overall just smaller, yet less archaic than ANA. They evolved in the direction of Proto-Mediterranean even before the Neolithic lifestyle kicked in. That's because they were living from small game, grains and were more sedentary, probably in larger groups, better organised, even before and early on admixed with WEA. The ANA and later IBM seem to have been more competitive on the individual level quite obviously, otherwise their specialisation would make little sense.
    That's quite a difference, regardless of potential small scale ANA admixture being real or not, which could have spread E too of course, even though I think its just less likely right now.

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    i was wrong the averge is of 1.3% not 1.2%
    and it was the averge of users not only europeans

    https://i.imgur.com/z5SUnvn.jpg


    p.s
    unfortuntely they geno 2 next do not exist since than

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    2 members found this post helpful.
    Anyone know the date of the oldest "E" ydna found in Eurasia, because we're talking here about the Caucasus 25,000 years ago. Also, wasn't Dzudzuana "C"? As the paper informs us, that sample and this one are pretty similar, so pretty close to 28% Basal Eurasian?

    Of course, we're all wildly speculating, but I've always been partial to the idea that the non-African haplogroups split up somewhere around Iran to South Asia. I think ydna "E" came later with the Ancient North Africans. That makes sense to me given the history of Egypt/N.E. Africa, North Africa, and the Natufians. I think they were Johnny come latelies.

    We could all be chasing our tails, because given the nature of men, Basal Eurasian may have been passed on by women after all the men were killed.

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    Quote Originally Posted by Angela View Post
    Anyone know the date of the oldest "E" ydna found in Eurasia, because we're talking here about the Caucasus 25,000 years ago. Also, wasn't Dzudzuana "C"? As the paper informs us, that sample and this one are pretty similar, so pretty close to 28% Basal Eurasian?

    Of course, we're all wildly speculating, but I've always been partial to the idea that the non-African haplogroups split up somewhere around Iran to South Asia. I think ydna "E" came later with the Ancient North Africans. That makes sense to me given the history of Egypt/N.E. Africa, North Africa, and the Natufians. I think they were Johnny come latelies.

    We could all be chasing our tails, because given the nature of men, Basal Eurasian may have been passed on by women after all the men were killed.



    late mesolithic

    e-z830

    https://genetiker.wordpress.com/2016...ent-near-east/

    https://i.imgur.com/AYYLYe1.png



    i think like you
    that it is more related to ANA than basal euroasian
    as much as i would like to think that y haplogroup E is related to basal ancestery
    that just don't fit

    https://en.wikipedia.org/wiki/Mesolithic

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    Quote Originally Posted by Angela View Post
    Anyone know the date of the oldest "E" ydna found in Eurasia, because we're talking here about the Caucasus 25,000 years ago. Also, wasn't Dzudzuana "C"? As the paper informs us, that sample and this one are pretty similar, so pretty close to 28% Basal Eurasian?

    Of course, we're all wildly speculating, but I've always been partial to the idea that the non-African haplogroups split up somewhere around Iran to South Asia. I think ydna "E" came later with the Ancient North Africans. That makes sense to me given the history of Egypt/N.E. Africa, North Africa, and the Natufians. I think they were Johnny come latelies.

    We could all be chasing our tails, because given the nature of men, Basal Eurasian may have been passed on by women after all the men were killed.
    The issue I think that the main body of ANA split very early from Basal Eurasian in a back migration or at least expansion into the rest of North and East Africa, either from the Levante-Near East or the Nile Region/North East Africa. I'd suppose that ANA and BEA would thus closer to each other, making E the preferable candidate for both to spread on the paternal side. I pretty much doubt E1b1b was in Africa before the next large scale back migration, which went through the region and created IBM, pushing the others South through the Green Sahara. So even in the case Natufians had an IBM influenced back migration of some sort introducing paternal lineages, it would still bring E1b1b closer to the BEA than to the local earlier E-carriers in Africa.
    Natufians just don't look like being heavily influenced by IBM-like people. Rather if, from a common source group for IBM and Natufians alike in North East Africa/Levante/South Arabia, which too was closer to Natufians and pre-Natufians in the Near East. We'll see.

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    the oldest E in Eurasia is Natufian
    in fact all E prior to the bronze age in Eurasia is E-M35
    this makes an origin for E-M35 outside of Africa very unlikely

    in the Dzudzuana paper Laziridis stated that there is no Yoruba DNA in Natufian or PPNB
    it is the other way around, Yoruba has some Dzudzuana, which probably travelled through the Levant

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    "a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe."


    Why 'parts of Europe'? Don't all Europeans have basal Eurasian ancestry?
    Most Europeans do not have Basal Eurasian ancestry because this ancestry peaks in indigenous Arabs such as the Bedouin. Near Eastern populations harbor more Basal Eurasian ancestry. Moreover, Basal Eurasians did not undergo much admixture with Neanderthals. Neanderthal ancestry is very low in native inhabitants of Arabia, which was out of the geographical Neanderthal range.




    Massive “Basal Eurasian” Back-Migration

    https://www.gnxp.com/WordPress/2020/...ack-migration/
    Last edited by ThirdTerm; 15-01-21 at 23:10.
    Давайте вместе снова сделаем мир великий!

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    1 members found this post helpful.
    in the Laziridis model Dzudzuana is 72 % Early West Eurasian + 28 % Basal Eurasian
    Early West Eurasian evolved into Villabrunan mainly through drift
    Early West Eurasian was IJ just before it split in I and J
    I crossed the Caucasus prior to the Gravettian.
    J stayed south of the Caucasus all the time, they provided the Early West Eurasian.
    IMO the Basal Eurasian was brought by G and H2, coming from the east (India or Indus Valley).

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    Quote Originally Posted by ThirdTerm View Post
    Most Europeans do not have Basal Eurasian ancestry because this ancestry peaks in indigenous Arabs such as the Bedouin. Near Eastern populations harbor more Basal Eurasian ancestry. Moreover, Basal Eurasians did not undergo much admixture with Neanderthals. Neanderthal ancestry is very low in native inhabitants of Arabia, which was out of the geographical Neanderthal range.


    Massive “Basal Eurasian” Back-Migration”
    the Neanderthal admixture happened in SW Asia though, not in Europe
    Neanderthals lived next to modern humans in the Zagros Mountains and the Levant for 30.000 years (80-50 ka)
    When modern humans arrived in Europe and Central Asia, Neanderthals got extinct soon after

    moreover the admixture happened 50-55 ka, modern humans didn't arrive in Europe and Central Asia before 50 ka

    halpogroup E did not mix with Neanderthals as Mota didn't have any Neanderthal DNA
    E-M35 got Neanderthal DNA when it arrived in the Levant

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    Quote Originally Posted by bicicleur 2 View Post
    in the Laziridis model Dzudzuana is 72 % Early West Eurasian + 28 % Basal Eurasian
    Early West Eurasian evolved into Villabrunan mainly through drift
    Early West Eurasian was IJ just before it split in I and J
    I crossed the Caucasus prior to the Gravettian.
    J stayed south of the Caucasus all the time, they provided the Early West Eurasian.
    IMO the Basal Eurasian was brought by G and H2, coming from the east (India or Indus Valley).
    That's exactly how I see it, as I said above, i.e. a bifurcation somewhere near India. That's how they had no Neanderthal. I might bet on H instead of G though.

    E is too young in West Eurasia to be responsible for 26,000 year old Basal Eurasian admixture in the Caucasus.

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