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Thread: A pre-LGM human lineage from the Caucasus was an ancestral component of West Eurasia

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    A pre-LGM human lineage from the Caucasus was an ancestral component of West Eurasia

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

    Highlights

    A single shotgun-sequenced Pleistocene sediment yielded genomic data of three mammals


    Sediment genome sequencing can produce data comparable to that from skeletal remains


    A pre-LGM human lineage from the Caucasus was an ancestral component of West Eurasia


    ∼0.01X wolf and bison environmental genomes, suggesting reshaping of populations


    Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental “shotgun” genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental 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 direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.


    https://www.sciencedirect.com/scienc...60982221008186

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    Can anyone post a link to the public data? I am currently searching for it.

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    Quote Originally Posted by Jovialis View Post
    Can anyone post a link to the public data? I am currently searching for it.

    as you i see nothing ( bummer)
    maybe in a frew more months or years

    https://www.ebi.ac.uk/ena/browser/view/PRJEB41420
    phenotype:
    gracile- med

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    Quote Originally Posted by kingjohn View Post
    as you i see nothing ( bummer)
    maybe in a frew more months or years

    https://www.ebi.ac.uk/ena/browser/view/PRJEB41420
    Thanks! let's keep on eye on the availability.

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    probably it will be similar to the teeth examined by Lazaridis in Dzudzuana

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    Quote Originally Posted by bicicleur 2 View Post
    probably it will be similar to the teeth examined by Lazaridis in Dzudzuana
    Indeed, this paper is a nice consolation for having to wait on the Lazaridis pre-print so long.

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    Quote Originally Posted by bicicleur 2 View Post
    probably it will be similar to the teeth examined by Lazaridis in Dzudzuana
    Tweet from the main author:



    Here is another interesting chart:


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    Quote Originally Posted by kingjohn View Post
    as you i see nothing ( bummer)
    maybe in a frew more months or years

    https://www.ebi.ac.uk/ena/browser/view/PRJEB41420
    Awww!


    According to Davidski there are plenty of new aDNA papers coming on things like the Eneolithic steppe, Rome, Greece, the Migration Period, the origins of Jews, the Uralic expansions. Knowing this info makes one even more impatient. COVID-19 upsets a lot of things, not only the everyday life.

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    SAT29 belongs to mtDNA haplogroup N like Dzudzuana3 from Dzudzuana cave. SAT29 shares more drift with Villabruna and Dzudzuana2, showing higher genetic affinity to Northern and Western Europeans. 1% Neanderthal ancestry in the SAT29 sample is lower than that of Palaeolithic Europeans due to dilution from Basal Eurasian ancestry, which is similar to Dzuzuana2.


    Давайте вместе снова сделаем мир великий!

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    Dodecad K12b

    Code:
    Pre-LGM_Caucasian:SAT29,7.46,0,14.24,0,0,0,8.5,21.29,0,0,48.51,0

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    Distance to: Pre-LGM_Caucasian:SAT29
    32.93469903 Turk_East_Black_Sea
    33.05443692 Turk_Ahiska
    33.17364315 Georgian
    33.18707881 Hemshin
    33.29327259 Abkhazian
    33.39283007 Georgian_Adjara
    33.40730010 Laz
    33.50200442 Georgian_Imereti
    33.59617687 Georgian_Gurian
    33.59877230 Turk_East
    33.66131905 Georgian_Mingrelian
    33.83854459 Greek_Pontus
    33.94612496 Ossetian_South
    33.98356073 Georgian_Svan
    34.06052114 Armenian_East
    34.60104623 Udi_Azerbaijan
    34.62249413 Ossetian
    34.72694775 Lebanese_Muslim
    34.80265076 Armenian_West
    34.84212393 Turk_Central_East
    34.84946341 Turk_Central_Black_Sea
    34.86093229 Adyghe
    34.86591746 Azerbaijani_Turkey
    35.17520291 Karachay
    35.28525613 Azerbaijani_Republic

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    Distance to: Pre-LGM_Caucasian:SAT29
    33.19415611 Turks
    33.70832835 Armenians
    33.81016711 Turkish
    34.07534886 Armenians_15
    34.37295448 Armenian
    35.12559466 Georgia_Jews
    35.31098129 Azerbaijan_Jews
    35.56283734 Balkars
    35.58838856 Uzbekistan_Jews
    35.68234017 North_Ossetians
    35.87307347 Kumyks
    35.91397221 Lebanese
    35.94649218 Druze
    36.08702537 Adygei
    36.16494712 Assyrian
    36.90931319 Iranian_Jews
    37.54196852 Abhkasians
    37.74577327 Iranian
    37.80515044 Jordanians
    37.83702684 Cypriots
    38.11466122 Kurd
    38.21836470 Iraq_Jews
    38.35201950 Kurds
    38.44894537 Chechens
    38.82187914 Egyptans

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    Distance to: Pre-LGM_Caucasian:SAT29
    33.36272171 Kura-Araxes_culture_(n=8)
    34.04441658 Chalcolithic_Azerbaijan_(n=4)
    34.32936207 Chalcolithic_Northwest_Caucasus_(n=3)
    35.52561611 Middle-Late_Bronze_Age_Hittites_(n=2)
    35.83805519 Early_Bronze_Age_Anatolia_(n=4)
    36.17485729 Middle-Late_Bronze_Age_North_Levant_(n=24)
    36.28659945 Chalcolithic_Anatolia_(n=35)
    38.30993474 Early-Middle_Bronze_Age_North_Levant_(n=9)
    38.77635104 Late_Bronze_Age_Israel_(n=3)
    40.33677107 Imperial-age_Latium_(East_Med_immigrants)_(n=46)
    40.80309179 Maykop_culture_(n=16)
    41.53297244 Caucasian_Alans_(n=2)
    41.60260208 Iron_Age_Armenia_(n=7)
    41.95314291 Middle_Bronze_Age_Anatolia_(n=2)
    42.13693866 Late_Bronze_Age_North_Caucasus_(n=4)
    42.45670265 Italian_Greeks_(n=2)
    42.60488352 Iron_Age_&_Hellenistic_Egypt_(n=3)
    44.21581278 Chalcolithic_North_Levant_(n=6)
    44.23648720 Epipaleolithic_Mesolithic_Caucasus_(CHG)_(n=2)
    46.86361275 6th-century_Piedmont_(Italians_only)_(n=7)
    46.91402029 Early_Bronze_Age_Jordan_(n=3)
    47.10485856 EMBA_Greece_(n=6)
    47.19817793 Imperial-age_Marche_(n=2)
    47.52351944 Medieval_Foggia_Apulia_(n=5)
    48.52816502 Pre-Pottery_Neolithic_Levant_(n=15)

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    Quote Originally Posted by Jovialis View Post
    Dodecad K12b

    Code:
    Pre-LGM_Caucasian:SAT29,7.46,0,14.24,0,0,0,8.5,21.29,0,0,48.51,0

    the significant east african and northwest african %
    might be just common southwest asian shared allells between
    sat29 and k12b calculator refernces ( it a modern calculator after all )

    and it is hard for him to deal with such an anciaent individual like this ancient caucasus lady

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    Quote Originally Posted by kingjohn View Post
    the significant east african and northwest african %
    might be just common southwest asian shared allells between
    sat29 and k12b calculator refernces ( it a modern calculator after all )

    and it is hard for him to deal with such an anciaent individual like this ancient caucasus lady
    There is probably a lot of Basal Eurasian in those populations, modern components are indeed not very reliable when looking at paleolithic samples. It is sort of like how Neanderthal is assigned a lot of SSA in K12b. It makes me wonder if the North African and East African in K12b found in samples that are unlikely to have them, are actually picking up some Basal Eurasian.

    At any rate, on the PCA for Dodecad Globe 13, SAT29 clusters between Anatolian_N and modern Sardinia; yet much closer to Anatolian_N:



    Dodecad Globe 13:

    Code:
    SAT29,0,0,0,0,0,0,55.35,0,0,0.11,0,0,44.55

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    However, when only using the aggregates for the modern populations, they do cluster further down on the "Z-axis", they are "north" of modern north Africans. Nevertheless, I maintain the idea that K12b is not accurately analyzing the components because they are based on modern populations.

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    SAT29 vs Paleolithic sample cohorts; they are significantly closest to CHG, albeit quiet distant:

    Distance to: Pre-LGM_Caucasian:SAT29
    44.23648720 Epipaleolithic_Mesolithic_Caucasus_(CHG)_(n=2)
    61.56415028 Epipaleolithic_Levant_(Natufians)_(n=6)
    67.90287107 Mesolithic_Anatolia_(AHG)_(n=1)
    71.94030650 Epipaleolithic_Magreb_(Iberomaurusians)_(n=5)
    91.68439616 Mesolithic_West_Europeans_(WHG)_(n=21)
    95.04796053 Mesolithic_Balkans_HG_(n=43)
    95.59985826 Mesolithic_Volga-Ural_(n=2)
    98.20644836 Mesolithic_Baltic_Scandinavia_(SHG)_(n=31)
    98.55494813 Mesolithic_Northwest_Russia_(n=4)
    99.37091979 Mesolithic_Ukraine_(n=7)
    100.05874724 Late_Mesolithic_Comb_Ceramic_culture_(n=2)

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    Quote Originally Posted by Jovialis View Post
    SAT29 vs Paleolithic sample cohorts; they are significantly closest to CHG, albeit quiet distant:

    Distance to: Pre-LGM_Caucasian:SAT29
    44.23648720 Epipaleolithic_Mesolithic_Caucasus_(CHG)_(n=2)
    61.56415028 Epipaleolithic_Levant_(Natufians)_(n=6)
    67.90287107 Mesolithic_Anatolia_(AHG)_(n=1)
    71.94030650 Epipaleolithic_Magreb_(Iberomaurusians)_(n=5)
    91.68439616 Mesolithic_West_Europeans_(WHG)_(n=21)
    95.04796053 Mesolithic_Balkans_HG_(n=43)
    95.59985826 Mesolithic_Volga-Ural_(n=2)
    98.20644836 Mesolithic_Baltic_Scandinavia_(SHG)_(n=31)
    98.55494813 Mesolithic_Northwest_Russia_(n=4)
    99.37091979 Mesolithic_Ukraine_(n=7)
    100.05874724 Late_Mesolithic_Comb_Ceramic_culture_(n=2)
    seems logical as CHG = Dzudzuana + ANE/EHG

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    Though I seriously doubt (I know) K12b can replicate it accurately, I am trying to find the components I could use to mirror the Lazaridis et al. 2018 pre-print with SAT29 in place of Dzudzuana.

    The only one I am missing is Russia_Baikal_EN

    Code:
    Villabruna,0,0,0,0,35.43,61.15,0,0,0,0,0,3.42
    Pre-LGM_Caucasian:SAT29,7.46,0,14.24,0,0,0,8.5,21.29,0,0,48.51,0
    ElMiron_Magdalenian_Spain,0,1.03,0,7.12,32.40,48.81,7.24,0.45,0,0,0,2.96
    AfontovaGora3_Russia,23.68,16.94,0,0,0,54.64,3.29,0,0,0,0,1.45
    Mbuti_(n=15),0.024,0.016,0,0.016,0,0.018,0.035333333,29.062,0,0.080666667,0.009333333,70.73866667

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    Doubt Russia_Baikal_EN would make a difference in modeling. It definitely doesn't resemble the results that the paper would produce, plus the fit is really distant.

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    Btw, does anyone know which study Russia_Baikal_EN is a part of?

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    Quote Originally Posted by kingjohn View Post
    Yes KingJohn. I think that the source it's this article that you posted the link access. Next I post another link to the same paper.

    https://www.cell.com/cell/pdf/S0092-8674(20)30502-X.pdf


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    Thanks guys, I'll get to it when I have a moment.

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